Variant report

Variant	rs2255496
Chromosome Location	chr6:101904442-101904443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101902345..101905078-chr6:101905414..101908161,2	K562	blood:
2	chr17:57920779..57923321-chr6:101903255..101904760,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1832415	1.00[YRI][hapmap]
rs2248237	0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs2248801	0.80[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2248950	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2249263	0.80[CEU][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap]
rs2252682	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2518155	1.00[YRI][hapmap]
rs2518160	0.92[CEU][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2518166	0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs2518167	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap]
rs2518168	0.81[CHB][hapmap]
rs2518169	0.81[CHB][hapmap]
rs2518170	0.80[CHB][hapmap]
rs2518171	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[TSI][hapmap];0.87[YRI][hapmap]
rs2518185	0.85[MEX][hapmap];1.00[YRI][hapmap]
rs2518229	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2518232	0.81[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518233	0.82[EUR][1000 genomes]
rs2579935	0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs2579939	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2788279	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs2788280	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2788282	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv886459	chr6:101880376-101951502	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886460	chr6:101890395-101951502	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2255496	SIM1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101902400-101907800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:101903400-101921000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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